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RNA structures (DSSR) / Stacking interactions in G-quadruplexes
« on: May 21, 2021, 05:19:10 am »
Dear Dr. Xiang-Jun Lu,
  I would like to ask you how to judge the pi-pi stacking interactions between nucleotides in the G-quadruplex structure. What is the distance between two aromatic bases to judge the strength of stack interactions? For example, the distance between them is considered to have strong stacking interaction in the range of nanometers, and it is considered to be weak stacking force in other ranges. Could you please give me some advice or help? Thank you very much. Looking forward to your reply.
 Best regards,
 zw Han.
 

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Recently, I have been struggling with a problem, that is, the definition of glycoside dihedral angle. I saw it the definition of glycosidic torsions( syn:(-90,90), anti:([-180,-90]&[90,180]) on the website(http://x3dna.org/). However, The book(Stephen Neidle - Principles of Nucleic Acid Structure-Elsevier_ Academic Press) has defined the glycosidic angles :
Anti: −120 > χ >180°
Syn: 0 < χ < 90°

So I wonder what the definition of glycoside angle is. Could you please give me some answers about glycoside angle? Thank you very much.

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.